In the mid 21st century, the human race is facing a test.
Genetic engineering has changed the world, and with huge profits, research had accelerated accordingly. An immortality gene no longer seemed like a mere dream. However, a lab sample containing this gene escaped, creating a new life-form that took in genetic material from the natural world, evolving into an enemy that began to invade the human world.
The Shaher are now a force capable of defeating human military forces, and both North and South American continents have fallen under their control. In Japan, the government has created a Samurai unit to oppose the Shaher, utilizing soldiers enhanced with nano-machines to connect with an armored exoskeleton.
It is at this point that Tsukahara Takemichi is assigned to the first platoon of the Samurai Force.